Mr. Icahn held 27.8 million shares in the online-auction company as of March 31.

In April, EBay said it worked out a deal with Mr. Icahn to end his months-long effort to get eBay to spin off payments unit PayPal. EBay agreed to make former AT&T Inc. Chief Executive David Dorman a director, and Mr. Icahn dropped support for two men he had nominated for eBay’s board.

The activist investor also raised his stake in Apple Inc. and decreased his stake in Netflix.

Mr. Icahn raised his holdings in Apple by 2.8 million shares to more than 7.5 million shares, increasing his bullish bet on the iPhone maker.

In April, Apple increased its share-repurchase authorization to $90 billion from the $60 billion level announced last year. The company also increased its quarterly dividend by about 8% and said it will split its stock 7-for-1 in June.

At the time, Mr. Icahn said he agreed completely with Apple’s plans to boost its buyback plan and said he is “extremely pleased” with the company’s quarterly results. He also said the stock “remains meaningfully undervalued” and that “many analysts fail to understand the company.”

Mr. Icahn gave up his fight in February to force Apple to boost its share-repurchase program by $50 billion. Before that, he had retreated from a demand that the consumer-technology giant load up on debt to fund a buyback three times that size.

As for Netflix, the filing showed that Mr. Icahn continued to decrease his holdings, leaving him with 2.2 million shares at the end of March. High-growth and momentum stocks such as Netflix have tumbled in recent weeks. Shares of Netflix have declined around 21% over the past three months.

Mr. Icahn also increased his stake in Herbalife by 33,515 shares to 17 million shares. Mr. Icahn has taken a big bet on the nutritional-supplement company, whose shares have declined around 22% so far this year. Herbalife was accused by hedge-fund manager William Ackman of being a pyramid scheme. In March, the Federal Trade Commission launched a civil investigation into Herbalife’s practices. The company said in response that it will cooperate fully with the FTC and that it’s confident it’s in compliance with the law.

In late April, The Wall Street Journal reported that Mr. Icahn and Mr. Ackman made up after clashing publicly over Herbalife and trading insults on national television. The two also “agreed to disagree” on Herbalife, with Mr. Icahn holding a huge bullish bet and Mr. Ackman holding a huge bearish bet.